A Snakemake workflow for large-scale SARS-CoV-2 analyses.
First, clone the repository:
git clone https://github.com/cbg-ethz/SARS-CoV-2_AnalysisIf needed, search for new samples using QuerySRAAccessions.ipynb.
The whole analysis can then be reproduced by executing the following line:
./run_pipeline.shThis will download the reads, compute coverages, call variants, and plot summary figures.